Quantum Computer Simulation of Protein Protonation

In attempts to simulate the protonation of proteins, a major challenge is that the number of protonation states grows rapidly as a function (2^<em>N</em>) of the number of protonation sites (<em>N</em>). Expression on the free energy of the protonation state as an <em>N</em>-site Ising model ─ using an empirical Generalized-Born model ─ allows a quantum computer to efficiently determine the important states at a given pH value and subsequently reconstruct the pH titration process at all sites. Compared with the exact results painstakingly obtained with classical computers, the results obtained using quantum computers show good agreement for staphylococcal nuclease and excellent agreement for &alpha;-lactalbumin. This work illustrates the effectiveness of quantum computers in sampling important physical states, which may be useful in attacking challenging biomolecular problems.